PNCC Compute Processing Resources

All data collected at PNCC is available to users in 2 formats – raw data and pre-processed (Motion Corrected and CTF Fit). For instructions to download the data see the FAQ page. 

In addition to downloading the data, Programmatic Proposal teams can have 1 team member request access to the PNCC Compute Nodes on the EMSL Supercomputer CASCADE with free allocations of 2,000 node hours per project. The badging process for access to the compute resources involves a required background check and can take a month or longer for Foreign Nationals but most US Citizens can be approved in less than a month. Contact the PNCC User Coordinator for information on how to request access to PNCC Compute on CASCADE. Once access is approved and you receive your Secure ID token, we will schedule an onboarding session with our PNCC Computing specialist to introduce you to the CASCADE system and job submission protocols, highlight paths to various cryo-EM software and script templates and confirm you can login and access your data.

Available software on CASCADE includes:

  • RELION (1, 2 & 3)
  • CisTEM
  • EMAN2
  • FREALIGN
  • DYNAMO
  • IMOD
  • EMClarity
  • MotionCorr 2
  • CTFFind4
  • PHENIX
  • Note that other software can be installed on request

The PNCC Compute Partition provides priority job staging for PNCC projects and consists of 56 nodes where each node has 2x 16GB V100 GPGPU, 16 Intel XEON CPU cores, 1 TB SSD, and 256GB memory and is linked to 3PB parallel filesystem via FDR Infiniband network. Standard priority access to the other normal CASCADE nodes (1380 CPU only nodes) is also provided with the same badging and login.

Data workflow